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Benito Merino D, Zehnle H, Teske A, Wegener G. Deep-branching ANME-1c archaea grow at the upper temperature limit of anaerobic oxidation of methane. Front Microbiol 2022; 13:988871. [PMID: 36212815 PMCID: PMC9539880 DOI: 10.3389/fmicb.2022.988871] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/15/2022] [Indexed: 01/03/2023] Open
Abstract
In seafloor sediments, the anaerobic oxidation of methane (AOM) consumes most of the methane formed in anoxic layers, preventing this greenhouse gas from reaching the water column and finally the atmosphere. AOM is performed by syntrophic consortia of specific anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). Cultures with diverse AOM partners exist at temperatures between 12°C and 60°C. Here, from hydrothermally heated sediments of the Guaymas Basin, we cultured deep-branching ANME-1c that grow in syntrophic consortia with Thermodesulfobacteria at 70°C. Like all ANME, ANME-1c oxidize methane using the methanogenesis pathway in reverse. As an uncommon feature, ANME-1c encode a nickel-iron hydrogenase. This hydrogenase has low expression during AOM and the partner Thermodesulfobacteria lack hydrogen-consuming hydrogenases. Therefore, it is unlikely that the partners exchange hydrogen during AOM. ANME-1c also does not consume hydrogen for methane formation, disputing a recent hypothesis on facultative methanogenesis. We hypothesize that the ANME-1c hydrogenase might have been present in the common ancestor of ANME-1 but lost its central metabolic function in ANME-1c archaea. For potential direct interspecies electron transfer (DIET), both partners encode and express genes coding for extracellular appendages and multiheme cytochromes. Thermodesulfobacteria encode and express an extracellular pentaheme cytochrome with high similarity to cytochromes of other syntrophic sulfate-reducing partner bacteria. ANME-1c might associate specifically to Thermodesulfobacteria, but their co-occurrence is so far only documented for heated sediments of the Gulf of California. However, in the deep seafloor, sulfate-methane interphases appear at temperatures up to 80°C, suggesting these as potential habitats for the partnership of ANME-1c and Thermodesulfobacteria.
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Affiliation(s)
- David Benito Merino
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Hanna Zehnle
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Andreas Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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Layer G, Jahn M, Moser J, Jahn D. Radical SAM Enzymes Involved in Tetrapyrrole Biosynthesis and Insertion. ACS BIO & MED CHEM AU 2022; 2:196-204. [PMID: 37101575 PMCID: PMC10114771 DOI: 10.1021/acsbiomedchemau.1c00061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
The anaerobic biosyntheses of heme, heme d 1, and bacteriochlorophyll all require the action of radical SAM enzymes. During heme biosynthesis in some bacteria, coproporphyrinogen III dehydrogenase (CgdH) catalyzes the decarboxylation of two propionate side chains of coproporphyrinogen III to the corresponding vinyl groups of protoporphyrinogen IX. Its solved crystal structure was the first published structure for a radical SAM enzyme. In bacteria, heme is inserted into enzymes by the cytoplasmic heme chaperone HemW, a radical SAM enzyme structurally highly related to CgdH. In an alternative heme biosynthesis route found in archaea and sulfate-reducing bacteria, the two radical SAM enzymes AhbC and AhbD catalyze the removal of two acetate groups (AhbC) or the decarboxylation of two propionate side chains (AhbD). NirJ, a close homologue of AhbC, is required for propionate side chain removal during the formation of heme d 1 in some denitrifying bacteria. Biosynthesis of the fifth ring (ring E) of all chlorophylls is based on an unusual six-electron oxidative cyclization step. The sophisticated conversion of Mg-protoporphyrin IX monomethylester to protochlorophyllide is facilitated by an oxygen-independent cyclase termed BchE, which is a cobalamin-dependent radical SAM enzyme. Most of the radical SAM enzymes involved in tetrapyrrole biosynthesis were recognized as such by Sofia et al. in 2001 (Nucleic Acids Res.2001, 29, 1097-1106) and were biochemically characterized thereafter. Although much has been achieved, the challenging tetrapyrrole substrates represent a limiting factor for enzyme/substrate cocrystallization and the ultimate elucidation of the corresponding enzyme mechanisms.
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Affiliation(s)
- Gunhild Layer
- Institut
für Pharmazeutische Wissenschaften, Pharmazeutische Biologie, Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Str. 19, 79104 Freiburg im Breisgau, Germany
- . Phone: ++49
0761 203 8373
| | - Martina Jahn
- Institut
für Mikrobiologie, Technische Universität
Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Jürgen Moser
- Institut
für Mikrobiologie, Technische Universität
Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Dieter Jahn
- Braunschweig
Integrated Center of Systems Biology BRICS, Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
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3
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Mattison RL, Bowyer AA, New EJ. Small molecule optical sensors for nickel: The quest for a universal nickel receptor. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213522] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Jasper J, Ramos JV, Trncik C, Jahn D, Einsle O, Layer G, Moser J. Chimeric Interaction of Nitrogenase-Like Reductases with the MoFe Protein of Nitrogenase. Chembiochem 2020; 21:1733-1741. [PMID: 31958206 PMCID: PMC7317204 DOI: 10.1002/cbic.201900759] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/17/2020] [Indexed: 11/24/2022]
Abstract
The engineering of transgenic organisms with the ability to fix nitrogen is an attractive possibility. However, oxygen sensitivity of nitrogenase, mainly conferred by the reductase component (NifH)2 , is an imminent problem. Nitrogenase-like enzymes involved in coenzyme F430 and chlorophyll biosynthesis utilize the highly homologous reductases (CfbC)2 and (ChlL)2 , respectively. Chimeric protein-protein interactions of these reductases with the catalytic component of nitrogenase (MoFe protein) did not support nitrogenase activity. Nucleotide-dependent association and dissociation of these complexes was investigated, but (CfbC)2 and wild-type (ChlL)2 showed no modulation of the binding affinity. By contrast, the interaction between the (ChlL)2 mutant Y127S and the MoFe protein was markedly increased in the presence of ATP (or ATP analogues) and reduced in the ADP state. Upon formation of the octameric (ChlL)2 MoFe(ChlL)2 complex, the ATPase activity of this variant is triggered, as seen in the homologous nitrogenase system. Thus, the described reductase(s) might be an attractive tool for further elucidation of the diverse functions of (NifH)2 and the rational design of a more robust reductase.
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Affiliation(s)
- Jan Jasper
- Institut für MikrobiologieTechnische Universität BraunschweigSpielmannstrasse 738106BraunschweigGermany
| | - José V. Ramos
- Institut für Pharmazeutische WissenschaftenPharmazeutische Biologie und BiotechnologieAlbert-Ludwigs-Universität FreiburgStefan-Meier-Str. 1979104FreiburgGermany
| | - Christian Trncik
- Institut für BiochemieAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179104FreiburgGermany
| | - Dieter Jahn
- Institut für MikrobiologieTechnische Universität BraunschweigSpielmannstrasse 738106BraunschweigGermany
| | - Oliver Einsle
- Institut für BiochemieAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179104FreiburgGermany
| | - Gunhild Layer
- Institut für Pharmazeutische WissenschaftenPharmazeutische Biologie und BiotechnologieAlbert-Ludwigs-Universität FreiburgStefan-Meier-Str. 1979104FreiburgGermany
| | - Jürgen Moser
- Institut für MikrobiologieTechnische Universität BraunschweigSpielmannstrasse 738106BraunschweigGermany
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Ghebreamlak SM, Mansoorabadi SO. Divergent Members of the Nitrogenase Superfamily: Tetrapyrrole Biosynthesis and Beyond. Chembiochem 2020; 21:1723-1728. [PMID: 32180329 DOI: 10.1002/cbic.201900782] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/13/2020] [Indexed: 11/06/2022]
Abstract
The nitrogenase superfamily constitutes a large and diverse ensemble of two-component metalloenzymes. These systems couple the hydrolysis of ATP to the reduction of disparate substrates from diatomic gases (Mo and alternative nitrogenases) to photosynthetic pigments (protochlorophyllide and chlorophyllide oxidoreductases). Only very recently have the activities of the highly divergent and paraphyletic Group IV nitrogenases begun to be uncovered. This review highlights the first characterized member of this group, which was found to catalyze an unprecedented reaction in the coenzyme F430 biosynthetic pathway, and the catalytic potential of a superfamily that has yet to be fully explored.
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Affiliation(s)
- Selamawit M Ghebreamlak
- Department of Chemistry and Biochemistry, Auburn University 179 Chemistry Building, Auburn, AL, 36849, USA
| | - Steven O Mansoorabadi
- Department of Chemistry and Biochemistry, Auburn University 179 Chemistry Building, Auburn, AL, 36849, USA
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Enzymatic Systems with Homology to Nitrogenase: Biosynthesis of Bacteriochlorophyll and Coenzyme F 430. Methods Mol Biol 2019; 1876:25-35. [PMID: 30317472 DOI: 10.1007/978-1-4939-8864-8_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Enzymes with homology to nitrogenase are essential for the reduction of chemically stable double bonds within the biosynthetic pathways of bacteriochlorophyll and coenzyme F430. These tetrapyrrole-based compounds are crucial for bacterial photosynthesis and the biogenesis of methane in methanogenic archaea. Formation of bacteriochlorophyll requires the unique ATP-dependent enzyme chlorophyllide oxidoreductase (COR) for the two-electron reduction of chlorophyllide to bacteriochlorophyllide. COR catalysis is based on the homodimeric protein subunit BchX2, which facilitates the transfer of electrons to the corresponding heterotetrameric catalytic subunit (BchY/BchZ)2. By analogy to the nitrogenase system, the dynamic switch protein BchX2 contains a [4Fe-4S] cluster that triggers the ATP-driven transfer of electrons onto a second [4Fe-4S] cluster located in (BchY/BchZ)2. The subsequent substrate reduction and protonation is unrelated to nitrogenase catalysis, with no further involvement of a molybdenum-containing cofactor. The biosynthesis of the nickel-containing coenzyme F430 includes the six-electron reduction of the tetrapyrrole macrocycle of Ni2+-sirohydrochlorin a,c-diamide to Ni2+-hexahydrosirohydrochlorin a,c-diamide catalyzed by CfbC/D. The homodimeric CfbC2 subunit carrying a [4Fe-4S] cluster shows close homology to BchX2. Accordingly, parallelism for the initial ATP-driven electron transfer steps of CfbC/D was proposed. Electrons are received by the dimeric catalytic subunit CfbD2, which contains a second [4Fe-4S] cluster and carries out the saturation of an overall of three double bonds in a highly orchestrated spatial and regioselective process. Following a short introduction to nitrogenase catalysis, this chapter will focus on the recent progress toward the understanding of the nitrogenase-like enzymes COR and CfbC/D, with special emphasis on the underlying enzymatic mechanism(s).
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A Preliminary Study of the Effect of Bioavailable Fe and Co on the Anaerobic Digestion of Rice Straw. ENERGIES 2019. [DOI: 10.3390/en12040577] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Rice straw is an abundant and sustainable substrate for anaerobic digestion (AD), but it is often deficient in essential trace elements (TEs) for proper microbial growth and metabolism. A lack of TEs leads to AD imbalances and suboptimal biogas yields. However, the total TE concentration is not a sufficient indicator of the amount of TEs available to the microorganisms. Therefore, this study investigated the degree of bioavailability of iron (Fe) and cobalt (Co) during the AD of rice straw, and correlated it to the biomethane yields and volatile fatty acids (VFAs) produced. When the two TEs were dosed at 205 µg Fe/g TS and 18 µg Co/g TS of rice straw, the biomethane production was approximately 260 mL CH4/g VS, i.e., similar to that obtained when Fe and Co were not added. Despite an increased bioavailable fraction of 23 and 48% for Fe and Co, respectively, after TEs addition, the AD performance was not enhanced. Moreover, VFAs did not exceed 250 mg HAc/L both in the presence and absence of added TEs, confirming no enhancement of the methanogenesis step. Therefore, the bioavailability of Fe and Co was not a limiting factor for the biomethane production at low total VFAs concentration.
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Identification of a unique Radical SAM methyltransferase required for the sp 3-C-methylation of an arginine residue of methyl-coenzyme M reductase. Sci Rep 2018; 8:7404. [PMID: 29743535 PMCID: PMC5943407 DOI: 10.1038/s41598-018-25716-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/27/2018] [Indexed: 12/27/2022] Open
Abstract
The biological formation of methane (methanogenesis) is a globally important process, which is exploited in biogas technology, but also contributes to global warming through the release of a potent greenhouse gas into the atmosphere. The last and methane-releasing step of methanogenesis is catalysed by the enzyme methyl-coenzyme M reductase (MCR), which carries several exceptional posttranslational amino acid modifications. Among these, a 5-C-(S)-methylarginine is located close to the active site of the enzyme. Here, we show that a unique Radical S-adenosyl-L-methionine (SAM) methyltransferase is required for the methylation of the arginine residue. The gene encoding the methyltransferase is currently annotated as “methanogenesis marker 10” whose function was unknown until now. The deletion of the methyltransferase gene ma4551 in Methanosarcina acetivorans WWM1 leads to the production of an active MCR lacking the C-5-methylation of the respective arginine residue. The growth behaviour of the corresponding M. acetivorans mutant strain and the biophysical characterization of the isolated MCR indicate that the methylated arginine is important for MCR stability under stress conditions.
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Mancini G, Papirio S, Riccardelli G, Lens PNL, Esposito G. Trace elements dosing and alkaline pretreatment in the anaerobic digestion of rice straw. BIORESOURCE TECHNOLOGY 2018; 247:897-903. [PMID: 30060428 DOI: 10.1016/j.biortech.2017.10.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 09/29/2017] [Accepted: 10/01/2017] [Indexed: 06/08/2023]
Abstract
The effect of trace elements (TEs) addition and NaOH pretreatment on the anaerobic digestion of rice straw was investigated in batch tests. Co, Ni and Se were added to the raw rice straw at different dosages. The NaOH pretreatment was applied to the rice straw both alone and in combination with the addition of TEs, in order to evaluate potential synergistic effects of the pretreatment and the TEs supplementation on the biogas production yields. The results obtained showed that the alkaline pretreatment was more effective than the TEs addition in increasing the cumulative biogas production, causing a 21.4% enhancement of the final biomethane yield, whereas the increase due to TEs dosing was not statistically significant. The analysis of volatile fatty acids (VFAs) confirmed that the NaOH pretreatment resulted in a higher production of VFAs, indicating an increased hydrolysis, while TEs addition did not cause significant changes in the VFA concentrations.
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Affiliation(s)
- Gabriele Mancini
- Department of Civil and Mechanical Engineering, University of Cassino and Southern Lazio, via Di Biasio 43, 03043 Cassino (FR), Italy; UNESCO-IHE, Westvest 7, 2611 AX Delft, The Netherlands.
| | - Stefano Papirio
- Department of Civil, Architectural and Environmental Engineering, University of Naples Federico II, via Claudio 21, 80125 Naples, Italy
| | - Gerardo Riccardelli
- Department of Civil and Mechanical Engineering, University of Cassino and Southern Lazio, via Di Biasio 43, 03043 Cassino (FR), Italy; UNESCO-IHE, Westvest 7, 2611 AX Delft, The Netherlands
| | - Piet N L Lens
- UNESCO-IHE, Westvest 7, 2611 AX Delft, The Netherlands
| | - Giovanni Esposito
- Department of Civil and Mechanical Engineering, University of Cassino and Southern Lazio, via Di Biasio 43, 03043 Cassino (FR), Italy
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Mu L, Zhang L, Zhu K, Ma J, Li A. Semi-continuous anaerobic digestion of extruded OFMSW: Process performance and energetics evaluation. BIORESOURCE TECHNOLOGY 2018; 247:103-115. [PMID: 28946083 DOI: 10.1016/j.biortech.2017.09.085] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 09/11/2017] [Accepted: 09/13/2017] [Indexed: 05/28/2023]
Abstract
Recently, extrusion press treatment shows some promising advantages for effectively separating of organic fraction of municipal solid waste (OFMSW) from the mixed MSW, which is critical for their following high-efficiency treatment. In this study, an extruded OFMSW obtained from a demonstrated MSW treatment plant was characterized, and submitted to a series of semi-continuous anaerobic experiments to examine its biodegradability and process stability. The results indicated that the extruded OFMSW was a desirable substrate with a high biochemical methane potential (BMP), balanced nutrients and reliable stability. For increasing organic loading rates (OLRs), feeding higher volatile solid (VS) contents in feedstock was much better than shortening the hydraulic retention times (HRTs), while excessively high contents caused a low biodegradability due to the mass transfer limitation. For energetics evaluation, a high electricity output of 129.19-156.37kWh/ton raw MSW was obtained, which was further improved by co-digestion with food waste.
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Affiliation(s)
- Lan Mu
- School of Environmental Science & Technology, Dalian University of Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Dalian 116024, Liaoning, China
| | - Lei Zhang
- School of Environmental Science & Technology, Dalian University of Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Dalian 116024, Liaoning, China.
| | - Kongyun Zhu
- School of Environmental Science & Technology, Dalian University of Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Dalian 116024, Liaoning, China
| | - Jiao Ma
- School of Environmental Science & Technology, Dalian University of Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Dalian 116024, Liaoning, China
| | - Aimin Li
- School of Environmental Science & Technology, Dalian University of Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Dalian 116024, Liaoning, China
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Layer G, Krausze J, Moser J. Reduction of Chemically Stable Multibonds: Nitrogenase-Like Biosynthesis of Tetrapyrroles. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 925:147-161. [DOI: 10.1007/5584_2016_175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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Thanh PM, Ketheesan B, Yan Z, Stuckey D. Trace metal speciation and bioavailability in anaerobic digestion: A review. Biotechnol Adv 2016; 34:122-36. [DOI: 10.1016/j.biotechadv.2015.12.006] [Citation(s) in RCA: 180] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 12/10/2015] [Accepted: 12/15/2015] [Indexed: 11/17/2022]
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Improving Biomethane Production and Mass Bioconversion of Corn Stover Anaerobic Digestion by Adding NaOH Pretreatment and Trace Elements. BIOMED RESEARCH INTERNATIONAL 2015; 2015:125241. [PMID: 26137469 PMCID: PMC4468275 DOI: 10.1155/2015/125241] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 01/17/2015] [Accepted: 02/03/2015] [Indexed: 11/17/2022]
Abstract
This research applied sodium hydroxide (NaOH) pretreatment and trace elements to improve biomethane production when using corn stover for anaerobic digestion. Full-factor experimental tests identified the best combination of trace elements with the NaOH pretreatment, indicating that the best combination was with 1.0, 0.4, and 0.4 mg·L(-1)·d(-1) of elements Fe, Co, and Ni, respectively. The cumulative biomethane production adding NaOH pretreatment and trace elements was 11,367 mL; total solid bioconversion rate was 55.7%, which was 41.8%-62.2% higher than with NaOH-pretreatment alone and 22.2%-56.3% higher than with untreated corn stover. The best combination was obtained 5-9 days shorter than T90 and maintained good system operation stability. Only a fraction of the trace elements in the best combination was present in the resulting solution; more than 85% of the total amounts added were transferred into the solid fraction. Adding 0.897 g of Fe, 0.389 g of Co, and 0.349 g of Ni satisfied anaerobic digestion needs and enhanced biological activity at the beginning of the operation. The results showed that NaOH pretreatment and adding trace elements improve corn stover biodegradability and enhance biomethane production.
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Welte C, Deppenmeier U. Bioenergetics and anaerobic respiratory chains of aceticlastic methanogens. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:1130-47. [PMID: 24333786 DOI: 10.1016/j.bbabio.2013.12.002] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 12/02/2013] [Accepted: 12/05/2013] [Indexed: 12/16/2022]
Abstract
Methane-forming archaea are strictly anaerobic microbes and are essential for global carbon fluxes since they perform the terminal step in breakdown of organic matter in the absence of oxygen. Major part of methane produced in nature derives from the methyl group of acetate. Only members of the genera Methanosarcina and Methanosaeta are able to use this substrate for methane formation and growth. Since the free energy change coupled to methanogenesis from acetate is only -36kJ/mol CH4, aceticlastic methanogens developed efficient energy-conserving systems to handle this thermodynamic limitation. The membrane bound electron transport system of aceticlastic methanogens is a complex branched respiratory chain that can accept electrons from hydrogen, reduced coenzyme F420 or reduced ferredoxin. The terminal electron acceptor of this anaerobic respiration is a mixed disulfide composed of coenzyme M and coenzyme B. Reduced ferredoxin has an important function under aceticlastic growth conditions and novel and well-established membrane complexes oxidizing ferredoxin will be discussed in depth. Membrane bound electron transport is connected to energy conservation by proton or sodium ion translocating enzymes (F420H2 dehydrogenase, Rnf complex, Ech hydrogenase, methanophenazine-reducing hydrogenase and heterodisulfide reductase). The resulting electrochemical ion gradient constitutes the driving force for adenosine triphosphate synthesis. Methanogenesis, electron transport, and the structure of key enzymes are discussed in this review leading to a concept of how aceticlastic methanogens make a living. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.
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Affiliation(s)
- Cornelia Welte
- Institute of Microbiology and Biotechnology, University of Bonn, Meckenheimer Allee 168, 53115 Bonn, Germany; Department of Microbiology, IWWR, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Uwe Deppenmeier
- Institute of Microbiology and Biotechnology, University of Bonn, Meckenheimer Allee 168, 53115 Bonn, Germany.
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Factors influencing the degradation of garbage in methanogenic bioreactors and impacts on biogas formation. Appl Microbiol Biotechnol 2012; 94:575-82. [DOI: 10.1007/s00253-012-3953-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 02/06/2012] [Accepted: 02/06/2012] [Indexed: 10/28/2022]
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16
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Knör G, Monkowius U. Photosensitization and photocatalysis in bioinorganic, bio-organometallic and biomimetic systems. ADVANCES IN INORGANIC CHEMISTRY 2011. [DOI: 10.1016/b978-0-12-385904-4.00005-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Pobeheim H, Munk B, Lindorfer H, Guebitz GM. Impact of nickel and cobalt on biogas production and process stability during semi-continuous anaerobic fermentation of a model substrate for maize silage. WATER RESEARCH 2011; 45:781-787. [PMID: 20875911 DOI: 10.1016/j.watres.2010.09.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Revised: 08/30/2010] [Accepted: 09/01/2010] [Indexed: 05/27/2023]
Abstract
The importance of nickel and cobalt on anaerobic degradation of a defined model substrate for maize was demonstrated. Five semi-continuous reactors were operated for 250 days at 35 °C and a well-defined trace metal solution was added to all reactors. Two reactors each were limited regarding the concentration of Ni(2+) and Co(2+), respectively, for certain time intervals. The required nickel concentration was depending on the organic loading rates (OLR) while, for example, above 2.6 g ODM L(-1) d(-1) nickel concentrations below 0.06 mg kg(-1) FM in the process significantly decreased biogas production by up to 25% compared to a control reactor containing 0.8 mg Ni(2+) kg(-1) FM. Similarly, limitation of cobalt to 0.02 mg kg(-1) FM decreased biogas production by about 10%. Limitations of nickel as well as cobalt lead to process instability. However, after gradual addition of nickel till 0.6 mg and cobalt till 0.05 mg kg(-1) FM the OLR was again increased to 4.3 g ODM L(-1) d(-1) while process stability was recovered and a fast metabolisation of acetic and propionic acid was detected. An increase of nickel to 0.88 mg kg(-1) FM did not enhance biogas performance. Furthermore, the increase of cobalt from 0.05 mg kg(-1) FM up to 0.07 mg kg(-1) FM did not exhibit a change in anaerobic fermentation and biogas production.
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Affiliation(s)
- Herbert Pobeheim
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
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Pobeheim H, Munk B, Müller H, Berg G, Guebitz GM. Characterization of an anaerobic population digesting a model substrate for maize in the presence of trace metals. CHEMOSPHERE 2010; 80:829-836. [PMID: 20615524 DOI: 10.1016/j.chemosphere.2010.06.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 06/06/2010] [Accepted: 06/07/2010] [Indexed: 05/29/2023]
Abstract
The influence of a defined trace metal solution and additionally Ni(2+) on anaerobic digestion of biomass was investigated. A novel synthetic model substrate was designed consisting of cellulose, starch and urea as carbon and nitrogen source in a ratio mimicking the basic composition of maize silage. Two independent batch fermentations were carried out over 21 d with the synthetic model substrate in the presence of the trace metal solution. Particularly an increase in nickel concentrations (17 and 34 microM) enhanced methane formation by up to 20%. This increased activity was also corroborated by fluorescence microscopy measurements based on cofactor F(420). The eubacterial and methanogenic population was characterized with the single strand conformational polymorphism analysis and the amplified 16S rDNA restriction analysis of 16S rRNA genes amplified by different primer systems. Nearly the half of the analyzed bacteria were identified as Firmicutes while 70% in this phylum belonged to the class of Clostridiales and 30% to the class of Bacilli. Bacteroides and uncultured bacteria represented each a quarter of the analyzed community. Methanogenic archaea were investigated with ARDRA, too. The hydrogenotrophic Methanoculleus sp. was the dominant genus which is commonly described for maize digestion thus confirming the value of the model substrate.
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Affiliation(s)
- Herbert Pobeheim
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
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19
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Affiliation(s)
- Yanjie Li
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Deborah B. Zamble
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
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20
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Zhang Y, Gladyshev VN. Comparative Genomics of Trace Elements: Emerging Dynamic View of Trace Element Utilization and Function. Chem Rev 2009; 109:4828-61. [DOI: 10.1021/cr800557s] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yan Zhang
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588-0664
| | - Vadim N. Gladyshev
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588-0664
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Ettwig KF, Shima S, van de Pas-Schoonen KT, Kahnt J, Medema MH, op den Camp HJM, Jetten MSM, Strous M. Denitrifying bacteria anaerobically oxidize methane in the absence ofArchaea. Environ Microbiol 2008; 10:3164-73. [DOI: 10.1111/j.1462-2920.2008.01724.x] [Citation(s) in RCA: 355] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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Heinemann IU, Jahn M, Jahn D. The biochemistry of heme biosynthesis. Arch Biochem Biophys 2008; 474:238-51. [PMID: 18314007 DOI: 10.1016/j.abb.2008.02.015] [Citation(s) in RCA: 226] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Revised: 02/14/2008] [Accepted: 02/14/2008] [Indexed: 02/03/2023]
Abstract
Heme is an integral part of proteins involved in multiple electron transport chains for energy recovery found in almost all forms of life. Moreover, heme is a cofactor of enzymes including catalases, peroxidases, cytochromes of the P(450) class and part of sensor molecules. Here the step-by-step biosynthesis of heme including involved enzymes, their mechanisms and detrimental health consequences caused by their failure are described. Unusual and challenging biochemistry including tRNA-dependent reactions, radical SAM enzymes and substrate derived cofactors are reported.
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Affiliation(s)
- Ilka U Heinemann
- Institute of Microbiology, Technical University of Braunschweig, Spielmannstr. 7, D-38106 Braunschweig, Germany
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23
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Zandvoort M, van Hullebusch E, Fermoso F, Lens P. Trace Metals in Anaerobic Granular Sludge Reactors: Bioavailability and Dosing Strategies. Eng Life Sci 2006. [DOI: 10.1002/elsc.200620129] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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24
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Guadalupe Hernández HJ, Pandiyan T, Bernes S. Mercaptoethanesulfonic acid (CoM imitator) interaction studies with nickel(II) complexes of pyridyl groups containing tetradentate ligands: Synthesis, structure, spectra and redox properties. Inorganica Chim Acta 2006. [DOI: 10.1016/j.ica.2005.09.036] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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25
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Tada C, Yang Y, Hanaoka T, Sonoda A, Ooi K, Sawayama S. Effect of natural zeolite on methane production for anaerobic digestion of ammonium rich organic sludge. BIORESOURCE TECHNOLOGY 2005; 96:459-464. [PMID: 15491827 DOI: 10.1016/j.biortech.2004.05.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2004] [Revised: 05/17/2004] [Accepted: 05/17/2004] [Indexed: 05/24/2023]
Abstract
The effect of an inorganic additive on the methane production from NH(4+)-rich organic sludge during anaerobic digestion was investigated using different kinds of inorganic adsorbent zeolites (mordenite, clinoptilolite, zeolite 3A, zeolite 4A), clay mineral (vermiculite), and manganese oxides (hollandite, birnessite). The additions of inorganic materials resulted in significant NH4+ removals from the natural organic sludge ([NH4+]=1, 150 mg N/l), except for the H-type zeolite 3A and birnessite. However, an enhanced methane production was only achieved using natural mordenite. Natural mordenite also enhanced the methane production from the sludge with a markedly high NH4+ concentration (4500 mg N/l) during anaerobic digestion. Chemical analyses of the sludge after the digestion showed considerable increases in the Ca2+ and Mg2+ concentrations in the presence of natural mordenite, but not with synthetic zeolite 3A. The effect of Ca2+ or Mg2+ addition on the methane production was studied using Na(+)-exchanges mordenite and Ca2+ or Mg(2+)-enriched sludge. The simultaneous addition of Ca2+ ions and Na(+)-exchanged mordenite enhanced the methane production; the amount of produced methane was about three times greater than that using only the Na(+)-exchanged mordenite. In addition, comparing the methane production by the addition of natural mordenite or Ca2+ ions, the methane production with natural mordenite was about 1.7 times higher than that with only Ca2+ ions. The addition of 5% and 10% natural mordenite were suitable condition for obtaining a high methane production. These results indicated that the Ca2+ ions, which are released from natural mordenite by a Ca2+/NH4+ exchange, enhanced the methane production of the organic waste at a high NH4+ concentration. Natural mordenite has a synergistic effect on the Ca2+ supply as well on the NH4+ removal during anaerobic digestion, which is effective for the mitigation of NH4+ inhibition against methane production.
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Affiliation(s)
- Chika Tada
- Biomass Research Group, Institute for Energy Utilization, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8569, Japan
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26
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Gonzalez-Gil G, Jansen S, Zandvoort MH, van Leeuwen HP. Effect of yeast extract on speciation and bioavailability of nickel and cobalt in anaerobic bioreactors. Biotechnol Bioeng 2003; 82:134-42. [PMID: 12584755 DOI: 10.1002/bit.10551] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The speciation of metals plays an important role in their bioavailability. In the case of anaerobic reactors for the treatment of wastewaters, the ubiquitous presence of sulfide leads to extensive precipitation of metals like nickel and cobalt, which are essential for the metabolism of the anaerobic microorganisms that carry out the mineralization of the pollutants present in the wastewater. In practice, nickel, cobalt, and iron are added in excessive amounts to full-scale installations. This study is concerned with the complexation of nickel and cobalt with yeast extract and its effect on the biogas production by methanogenic biomass. Adsorptive stripping voltammetry (AdSV) was used to get information about the stability and complexing capacity of the metal-yeast extract complexes formed. Nickel and cobalt form relatively strong organic complexes with yeast extract. The bioavailability of these essential metals in anaerobic batch reactors was dramatically increased by the addition of yeast extract. This is due to the formation of dissolved bioavailable complexes, which favors the dissolution of metals from their sulfides. Trace doses of yeast extract may be effective in keeping additions of essential metals to anaerobic reactors at a minimum.
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Affiliation(s)
- G Gonzalez-Gil
- Laboratory of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6703HB Wageningen, The Netherlands.
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27
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Pandiyan T, Consuelo-Estrada V, Moreno-Esparza R, Ruiz-Ramı́rez L. Mercaptoethanesulfonic acid studies with nickel(II) complexes of tetra- and hexadentate ligands containing pyridyl groups: synthesis, structure, spectra and redox behavior. Inorganica Chim Acta 2003. [DOI: 10.1016/s0020-1693(02)01194-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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28
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Bentley R, Chasteen TG. Microbial methylation of metalloids: arsenic, antimony, and bismuth. Microbiol Mol Biol Rev 2002; 66:250-71. [PMID: 12040126 PMCID: PMC120786 DOI: 10.1128/mmbr.66.2.250-271.2002] [Citation(s) in RCA: 299] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A significant 19th century public health problem was that the inhabitants of many houses containing wallpaper decorated with green arsenical pigments experienced illness and death. The problem was caused by certain fungi that grew in the presence of inorganic arsenic to form a toxic, garlic-odored gas. The garlic odor was actually put to use in a very delicate microbiological test for arsenic. In 1933, the gas was shown to be trimethylarsine. It was not until 1971 that arsenic methylation by bacteria was demonstrated. Further research in biomethylation has been facilitated by the development of delicate techniques for the determination of arsenic species. As described in this review, many microorganisms (bacteria, fungi, and yeasts) and animals are now known to biomethylate arsenic, forming both volatile (e.g., methylarsines) and nonvolatile (e.g., methylarsonic acid and dimethylarsinic acid) compounds. The enzymatic mechanisms for this biomethylation are discussed. The microbial conversion of sodium arsenate to trimethylarsine proceeds by alternate reduction and methylation steps, with S-adenosylmethionine as the usual methyl donor. Thiols have important roles in the reductions. In anaerobic bacteria, methylcobalamin may be the donor. The other metalloid elements of the periodic table group 15, antimony and bismuth, also undergo biomethylation to some extent. Trimethylstibine formation by microorganisms is now well established, but this process apparently does not occur in animals. Formation of trimethylbismuth by microorganisms has been reported in a few cases. Microbial methylation plays important roles in the biogeochemical cycling of these metalloid elements and possibly in their detoxification. The wheel has come full circle, and public health considerations are again important.
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Affiliation(s)
- Ronald Bentley
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.
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29
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30
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Stolzenberg AM, Zhang Z. F430 Model Chemistry. An Investigation of Nickel Complexes as Catalysts for the Reduction of Alkyl Halides and Methyl Coenzyme-M by Sodium Borohydride. Inorg Chem 1997. [DOI: 10.1021/ic960768d] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alan M. Stolzenberg
- Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506
| | - Zhong Zhang
- Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506
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31
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Pandiyan T, Bernés S, Durán de Bazúa C. Structure, spectra and redox studies of nickel(II) bis(benzimidazole-2-ylmethyl)amines with coenzyme M reductase. Polyhedron 1997. [DOI: 10.1016/s0277-5387(97)00007-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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32
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Kim JS, Reibenspies JH, Darensbourg MY. Lightinduced sulfur-dealkylation of phosphino-thioether nickel(0) complexes. Inorganica Chim Acta 1996. [DOI: 10.1016/s0020-1693(96)05237-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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33
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Zhang Z, Petersen JL, Stolzenberg AM. F430 Model Chemistry. A Reexamination of the [1,4,7,10,13-Pentaazacyclohexadecane-14,16-dionato(2−)]nickel(II)-Induced Formation of Methane from Methyl Coenzyme-M. Inorg Chem 1996. [DOI: 10.1021/ic960263n] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhong Zhang
- Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506
| | - Jeffrey L. Petersen
- Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506
| | - Alan M. Stolzenberg
- Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506
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34
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Kumar M, Qiu D, Spiro TG, Ragsdale SW. A methylnickel intermediate in a bimetallic mechanism of acetyl-coenzyme A synthesis by anaerobic bacteria. Science 1995; 270:628-30. [PMID: 7570019 DOI: 10.1126/science.270.5236.628] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Resonance Raman (RR) spectroscopy was used to identify a methylnickel adduct (upsilon Ni-C = 422 wave numbers) of carbon monoxide dehydrogenase (CODH) from Clostridium thermoaceticum. Formed at a nickel/iron-sulfur cluster on CODH called center A, the methylnickel species is the precursor of the methyl group of acetyl-coenzyme A in an anaerobic pathway of carbon monoxide or carbon dioxide fixation. Rapid kinetic and RR studies demonstrated that methylation of nickel occurs by heterolysis of the methyl-cobalt bond (upsilon Co-C = 429 wave numbers) of a methylated corrinoid/iron-sulfur protein. In combination with the earlier finding of an iron-carbonyl adduct at center A, detection of the methylnickel intermediate establishes a bimetallic mechanism for acetyl-coenzyme A synthesis.
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Affiliation(s)
- M Kumar
- Department of Biochemistry, Beadle Center, University of Nebraska, Lincoln 68588-0664, USA
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35
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Stroup D, Reeve JN. Association of the mcrD gene product with methyl coenzyme M reductase in Methanococcus vannielii. BIOCHIMICA ET BIOPHYSICA ACTA 1993; 1203:175-83. [PMID: 8268197 DOI: 10.1016/0167-4838(93)90080-b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The mcrD gene, subcloned from the methyl coenzyme M reductase (MR) encoding mcrBDCGA operon in Methanococcus vannielii, has been expressed at a high level in Escherichia coli. Rabbit antibodies, raised against the product of this gene (rgpmcrD, recombinant gene product of mcrD) purified from E. coli, have been used to quantitate gpmcrD in M. vannielii and to follow its fate during MR purification. The molar ratio of gpmcrD to MR was found to be approx. 1:15 in cells of M. vannielii taken from batch cultures at all stages of growth. Sedimentation of lysates of M. vannielii cells through sucrose gradients and analyses of the fractions obtained by Western blotting and immunoprecipitation have demonstrated the presence of a macromolecular complex containing both gpmcrD and MR. Addition of mcrD antibodies or removal of gpmcrD from lysates of M. vannielii cells by immunoprecipitation decreased the rates of methanogenesis in vitro by approx. 20%. Addition of purified rgpmcrD to these lysates did not stimulate methanogenesis.
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Affiliation(s)
- D Stroup
- Department of Microbiology, Ohio State University, Columbus 43210
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36
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Brenner M, Zhang H, Scott R. Nature of the low activity of S-methyl-coenzyme M reductase as determined by active site titrations. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(17)46653-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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37
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Zimmer M. Empirical force field analysis of the revised structure of coenzyme F430. Epimerization and geometry of the corphinoid tetrapyrrole. J Biomol Struct Dyn 1993; 11:203-14. [PMID: 8216945 DOI: 10.1080/07391102.1993.10508718] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We undertook an empirical force field analysis of the conformational changes that accompany the diepimerization of coenzyme F430. The crystal structure of 12,13-diepi F430M was used as a test of the parameter set and as the basis for the calculations. The individual pyrrole rings in 13-epi and 12,13-diepi F430 adopt alternating half chair conformations leading to a ruffled macrocycle, native F430 is also ruffled but the individual pyrroles are planar. The 12,13 di-dehydro F430 and native F430 conformations are extremely similar, this accounts for the experimental observation that reduction of 12,13 di-dehydro-F430 forms native F430 and not 12,13-diepi F430. Native F430 can easily accommodate both square planar and, by bending, trigonal bipyramidal coordination geometries about nickel. We suggest that bent trigonal bipyramidal form is the conformer bound to the protein and that direct binding of the amino acid side chains to nickel is probably not important.
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Affiliation(s)
- M Zimmer
- Chemistry Department, Connecticut College, New London 06320
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38
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Abstract
The polypeptide encoded by the mcrC gene has been identified in Methanococcus vannielii by immunoblotting using rabbit antibodies raised against the product of a lacZ-mcrC gene fusion synthesized and purified from Escherichia coli. The mcrC gene product (gpmcrC) was located in both the supernatant and pellet fractions after centrifugation of Mc. vannielii cell extracts for 2 h at 100,000 x g. When anaerobic reducing conditions were maintained during purification, gpmcrC co-sedimented through sucrose gradients to the same position as molecules of the methyl coenzyme M reductase holoenzyme (approx. 300 kDa). This co-sedimentation was lost under aerobic, nonreducing conditions.
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Affiliation(s)
- D Stroup
- Department of Microbiology, Ohio State University, Columbus
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39
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Chapter 4 Bioenergetics and transport in methanogens and related thermophilic archaea. ACTA ACUST UNITED AC 1993. [DOI: 10.1016/s0167-7306(08)60253-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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40
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Rospert S, Voges M, Berkessel A, Albracht SP, Thauer RK. Substrate-analogue-induced changes in the nickel-EPR spectrum of active methyl-coenzyme-M reductase from Methanobacterium thermoautotrophicum. EUROPEAN JOURNAL OF BIOCHEMISTRY 1992; 210:101-7. [PMID: 1332856 DOI: 10.1111/j.1432-1033.1992.tb17396.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Methyl-coenzyme-M reductase (MCR) catalyzes the formation of methane from methyl-coenzyme M [2-(methylthio)ethanesulfonate] and 7-mercaptoheptanoylthreonine phosphate in methanogenic archaea. The enzyme contains the nickel porphinoid coenzyme F430 as a prosthetic group. In the active, reduced (red) state, the enzyme displays two characteristic EPR signals, MCR-red1 and MCR-red2, probably derived from Ni(I). In the presence of the substrate methyl-coenzyme M, the rhombic MCR-red2 signal is quantitatively converted to the axial MCR-red1 signal. We report here on the effects of inhibitory substrate analogues on the EPR spectrum of the enzyme. 3-Bromopropanesulfonate (BrPrSO3), which is the most potent inhibitor of MCR known to date (apparent Ki = 0.05 microM), converted the EPR signals MCR-red1 and MCR-red2 to a novel axial Ni(I) signal designated MCR-BrPrSO3. 3-Fluoropropanesulfonate (apparent Ki < 50 microM) and 3-iodopropanesulfonate (apparent Ki < 1 microM) induced a signal identical to that induced by BrPrSO3 without affecting the line shape, despite the fact that the fluorine, bromine and iodine isotopes employed have nuclear spins of I = 1/2, I = 3/2 and I = 5/2, respectively. This finding suggests that MCR-BrPrSO3 is not the result of a close halogen-Ni(I) interaction. 7-Bromoheptanoylthreonine phosphate (BrHpoThrP) (apparent Ki = 5 microM), which is an inhibitory substrate analogue of 7-mercaptoheptanoylthreonine phosphate, converted the signals MCR-red1 and MCR-red2 to a novel axial Ni(I) signal, MCR-BrHpoThrP, similar but not identical to MCR-BrPrSO3. The results indicate that inhibition of MCR by the halogenated substrate analogues investigated above is not via oxidation of Ni(I)F430. The different MCR EPR signals are assigned to different enzyme/substrate and enzyme/inhibitor complexes.
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Affiliation(s)
- S Rospert
- Laboratorium für Mikrobiologie des Fachbereichs Biologie, Philipps-Universität, Marburg, Federal Republic of Germany
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41
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Brenner MC, Ma L, Johnson MK, Scott RA. Spectroscopic characterization of the alternate form of S-methylcoenzyme M reductase from Methanobacterium thermoautotrophicum (strain delta H). BIOCHIMICA ET BIOPHYSICA ACTA 1992; 1120:160-6. [PMID: 1314088 DOI: 10.1016/0167-4838(92)90264-e] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Two forms (MR1 and MR2) of S-methylcoenzyme M reductase were purified from Methanobacterium thermoautotrophicum (strain delta H) as recently described (Rospert, S., Linder, D., Ellerman, J. and Thauer, R.K. (1990) Eur. J. Biochem. 194, 871-877). MR2 was at least 50-fold more active than MR1, independent of assay conditions. The two forms are spectroscopically similar, but not identical, by UV-visible, magnetic circular dichroism and resonance Raman spectroscopies. MR2 exhibited an EPR signal corresponding to 20% of the enzyme-bound nickel. Strong EPR signals similar to those previously assigned to Ni(I)F430 bound to methylreductase in Methanobacterium thermoautotrophicum (strain Marburg) (Albracht, S.P.J., Ankel-Fuchs, D., Bocher, R., Ellerman, J., Moll, J., Van der Zwann, J.W. and Thauer, R.K. (1988) Biochim. Biophys. Acta 955, 86-102) were observed in MR2-rich, log-phase, as well as in MR1-rich, slow-growing bacteria. Log-phase cells had dramatically different EPR spectra depending on whether they were removed from the fermenter (under gas flow) before or after cooling to 10 degrees C. EPR spectra of slow-growing cells were insensitive to harvesting conditions. The possible biological significance of the alternate form of methylreductase is discussed.
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Affiliation(s)
- M C Brenner
- Department of Chemistry, University of Georgia, Athens 30602
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42
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Rospert S, Breitung J, Ma K, Schwörer B, Zirngibl C, Thauer RK, Linder D, Huber R, Stetter KO. Methyl-coenzyme M reductase and other enzymes involved in methanogenesis from CO2 and H2 in the extreme thermophile Methanopyrus kandleri. Arch Microbiol 1991; 156:49-55. [PMID: 1772346 DOI: 10.1007/bf00418187] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Methanopyrus kandleri belongs to a novel group of abyssal methanogenic archaebacteria that can grow at 110 degrees C on H2 and CO2 and that shows no close phylogenetic relationship to any methanogen known so far. Methyl-coenzyme M reductase, the enzyme catalyzing the methane forming step in the energy metabolism of methanogens, was purified from this hyperthermophile. The yellow protein with an absorption maximum at 425 nm was found to be similar to the methyl-coenzyme M reductase from other methanogenic bacteria in that it was composed each of two alpha-, beta- and gamma-subunits and that it contained the nickel porphinoid coenzyme F430 as prosthetic group. The purified reductase was inactive. The N-terminal amino acid sequence of the gamma-subunit was determined. A comparison with the N-terminal sequences of the gamma-subunit of methyl-coenzyme M reductases from other methanogenic bacteria revealed a high degree of similarity. Besides methyl-coenzyme M reductase cell extracts of M. kandleri were shown to contain the following enzyme activities involved in methanogenesis from CO2 (apparent Vmax at 65 degrees C): formylmethanofuran dehydrogenase, 0.3 U/mg protein; formyl-methanofuran:tetrahydro-methanopterin formyltransferase, 13 U/mg; N5,N10-methylenetetrahydromethanopterin cyclohydrolase, 14U/mg; N5,N10-methenyltetrahydromethanopterin dehydrogenase (H2-forming), 33 U/mg; N5,N10-methylenetetrahydromethanopterin reductase (coenzyme F420 dependent), 4 U/mg; heterodisulfide reductase, 2 U/mg; coenzyme F420-reducing hydrogenase, 0.01 U/mg; and methylviologen-reducing hydrogenase, 2.5 U/mg. Apparent Km values for these enzymes and the effect of salts on their activities were determined. The coenzyme F420 present in M. kandleri was identified as coenzyme F420-2 with 2-gamma-glutamyl residues.
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Affiliation(s)
- S Rospert
- Laboratorium für Mikrobiologie, Fachbereich Biologie, Philipps-Universität Marburg, Marburg/Lahn, Federal Republic of Germany
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